detailed_config.RmdRtD3 has a number of features that are not required, but can improve the output of a visualization.
These features include:
We will prepare the geoData by resolving the USA name conflict between the geoData and estimates.
geoData <- rnaturalearth::ne_countries(returnclass = 'sf') geoData <- geoData %>% mutate(sovereignt = ifelse(sovereignt == 'United States of America', 'United States', sovereignt))
We will also add a second data source (Cases and Deaths) to the rtData.
base_url <- 'https://raw.githubusercontent.com/epiforecasts/covid-rt-estimates/master/national/' summaryData <- readr::read_csv(paste0(base_url, 'cases/summary/summary_table.csv'), col_types = cols()) rtData <- readr::read_csv(paste0(base_url, 'cases/summary/rt.csv'), col_types = cols()) casesInfectionData <- readr::read_csv(paste0(base_url, 'cases/summary/cases_by_infection.csv'), col_types = cols()) casesReportData <- readr::read_csv(paste0(base_url, 'cases/summary/cases_by_report.csv'), col_types = cols()) obsCasesData <- readr::read_csv(paste0(base_url, 'cases/summary/reported_cases.csv'), col_types = cols()) rtData_death <- readr::read_csv(paste0(base_url, 'deaths/summary/rt.csv'), col_types = cols()) casesInfectionData_death <- readr::read_csv(paste0(base_url, 'deaths/summary/cases_by_infection.csv'), col_types = cols()) casesReportData_death <- readr::read_csv(paste0(base_url, 'deaths/summary/cases_by_report.csv'), col_types = cols()) obsCasesData_death <- readr::read_csv(paste0(base_url, 'deaths/summary/reported_cases.csv'), col_types = cols())
Here, rtData will have two items, “Cases” and “Deaths”. These labels are flexible and are passed to the dataset selector dropdown.
rtData = list('Cases' = list('rtData' = rtData, 'casesInfectionData' = casesInfectionData, 'casesReportData' = casesReportData, 'obsCasesData' = obsCasesData), 'Deaths' = list('rtData' = rtData_death, 'casesInfectionData' = casesInfectionData_death, 'casesReportData' = casesReportData_death, 'obsCasesData' = obsCasesData_death))
We can also configure a list of URLs to link more detailed estimates.
subregional_ref <- list('Afghanistan' = 'https://epiforecasts.io/covid/posts/national/afghanistan/', 'Brazil' = 'https://epiforecasts.io/covid/posts/national/brazil/', 'Colombia' = 'https://epiforecasts.io/covid/posts/national/colombia/', 'India' = 'https://epiforecasts.io/covid/posts/national/india/', 'Italy' = 'https://epiforecasts.io/covid/posts/national/italy/', 'Germany' = 'https://epiforecasts.io/covid/posts/national/germany/', 'Russia' = 'https://epiforecasts.io/covid/posts/national/russia/', 'United Kingdom' = 'https://epiforecasts.io/covid/posts/national/united-kingdom/', 'United States of America' = 'https://epiforecasts.io/covid/posts/national/united-states/')
The data and config are then passed to RtD3::summaryWidget.
## Warning in name_warning_geoData(name_diff): The following names are present
## in the estimates but not in the GeoData: Andorra, Antigua & Barbuda, Aruba,
## Bahamas, Bahrain ... and 33 more.